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select

The gamtools select tool is used to select or exclude samples from a :ref:`segregation table <segregation_table>`.

Usage and option summary

Usage:

gamtools select [OPTIONS] -s <SEGREGATION_FILE> -o <OUTPUT_FILE>
                          -n [<SAMPLE_NAME> [<SAMPLE_NAME> ...]]

Required parameters:

Option Description
-s, --segregation-file A file containing the segregation of all samples
-n, --sample-names Names of the samples to remove
-o, --output-file Output file path (or - to write to stdout)

Optional parameters:

Option Description
-d, --drop-samples Discard the listed samples (default: discard samples not in the list)